MolNFT v1 · #66114 · protein
Apo structure of pseudomonas aeruginosa isochorismate-pyruvate lyase I87T mutant
3HGW · Salicylate biosynthesis protein pchb: “Apo structure of pseudomonas aeruginosa isochorismate-pyruvate lyase I87T mutant”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.78). MolNFT v1 #66114 on GenesisL1: 3D…
- PDB
- 3HGW
- Type
- protein
- Length
- 336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Salicylate biosynthesis protein pchb
- EC
- 4.1.99.-
- UniProt
- Q51507
- Ligands
- CA
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Salicylate biosynthesis protein pchb (EC 4.1.99.-) | protein | 83 | 77% helix, 0% strand | Q51507 |
| D | Salicylate biosynthesis protein pchb (EC 4.1.99.-) | protein | 97 | 79% helix, 0% strand | Q51507 |
| A | Salicylate biosynthesis protein pchb (EC 4.1.99.-) | protein | 81 | 81% helix, 0% strand | Q51507 |
| B | Salicylate biosynthesis protein pchb (EC 4.1.99.-) | protein | 75 | 88% helix, 0% strand | Q51507 |
Ligands and binding sites
- CA · Calcium ion · metal · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.78 | 0.98 | 19 | empty |
| 2 | 253 | 0.58 | 0.79 | 34 | empty |
| 3 | 118 | 0.46 | 0.78 | 18 | empty |
| 4 | 118 | 0.43 | 0.77 | 18 | empty |
| 5 | 113 | 0.42 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2270 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2194 Ų buried · 22 hydrogen bonds · protein-protein
- C–B · 473 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 464 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 291 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HGW · Apo Structure of Pseudomonas aeruginosa Isochorismate-Pyruvate Lyase I87T mutant · the same entry in another collection · chain B against B, TM-score 1.00
- Q51507 · AlphaFold monomer V2.0 prediction for isochorismate pyruvate lyase (Q51507) · a predicted model of the same protein · chain C against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q51507
- Elsewhere: RCSB PDB 3HGW · PDBe 3HGW · UniProt Q51507
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